Overall I'm leaning towards the pixel art but here's my thoughts for both of them.
PIXEL ART VERSION:
+ The buildings look more 3D and the dome itself looks more like it's made of transparent glass.
+ The pixel art also handles gradients better for smoother color transitions.
+ Better-looking stars.
- Not a big fan of the moon-looking background -- looks like a wheel of swiss cheese or even a painter's palette.
VOXEL VERSION:
+ If your game were being made for mobile platforms, this would offer the greatest contrast. One of my biggest pet-peeves with ios games are ones with poor color contrast when you're trying to play on something like a small iPhone SE.
+ The cloudy background is much better.
- The stars now look like "X" cancel buttons like you would see to close out a window.
- The glass domes don't look as transparent.